The invention relates to the isolation of ions of a predefined narrow range of charge-related masses m/z in an RF quadrupole ion trap by removal of all other ions. The process of keeping “desired” ions, usually ions of a predefined narrow range of charge-related masses m/z, inside an ion trap while removing all “undesired” ions is called “isolation”. The usually narrow mass range of desired ions is denominated an “isolation window”. Quite often ions of a single mass or all ions of an isotope group are isolated. The purpose of isolation usually is the provision of analyte ions of one single type for further chemical or physical reactions and subsequent analysis of the reaction products, e.g. fragmentation and analysis of the fragment ions, without the presence of other types of ions which may disturb the analytical results. Fragment ions or reaction product ions can be used to study molecular structures (e.g. amino acid sequences) or chemical behavior of analyte ions.
Usually the undesired ions are “eliminated” (or “removed”) by resonant excitation which increases their oscillation amplitudes until they collide with the electrodes of the ion trap, thereby discharging and destroying the ions. Elegant elimination methods use complex mixtures of excitation frequencies to eliminate most of (or even all) the undesired ions simultaneously. Such mixtures of excitation frequencies are often called “broadband waveforms” or “waveform signals”. The first application of such waveforms goes back to A. Marshall et al. (U.S. Pat. No. 4,761,545; 1988). Marshall et al. excited ions inside ion cyclotron resonance cells by mixtures of excitation frequencies (SWIFT=Stored Waveform [calculated by] Inverse Fourier Transformation). The term “stored waveform” refers to a digital storage memory, from which digital values are transferred, in fast sequence, to a digital-to-analog converter (DAC), connected to excitation electrodes. The DAC then delivers the frequency mixture as an output. Modern applications of such frequency mixtures for ion isolation in RF ion traps are described in documents U.S. Pat. No. 7,456,396 B2 (S. T. Quarmby et al., 2004: “Isolating Ions in Quadrupole Ion Traps for Mass Spectrometry”) and U.S. Pat. No. 7,378,648 B2 (M. Wang et al., 2005: “High Resolution Ion Isolation Utilizing Broadband Waveform Signals”). These methods of synchronous elimination of most or all undesired ions usually work well.
RF quadrupole ion traps can be used as mass spectrometers, in two-dimensional as well as in three-dimensional form. The two-dimensional quadrupole ion trap of FIG. 1 (often called a “linear ion trap”) shows four rod electrodes (1 to 4) with hyperbolic surfaces; at the ends, two apertured diaphragms usually close the inner volume (not shown in FIG. 1). The three-dimensional ion trap of FIG. 2 consists of two endcap electrodes (11, 13) and one ring electrode (12); both types of electrodes with rotationally hyperbolic surfaces. The ion traps are operated with RF voltages up to 30 kilovolts peak to peak and frequencies of around one megahertz, forming inside quadrupolar pseudopotential wells in two or three dimensions, in which the ions can oscillate as in a real potential well. All types of RF ion traps are operated with a damping gas of a pressure of around one pascal to damp (“cool”) the oscillations of the ions within the pseudopotential well of the trap so that they gather in the center. The damping process decreases the oscillation amplitudes exponentially with a time constant of about one millisecond. Ions can be ejected from the center mass-sequentially (in sequence of increasing charge-related masses m/z) through apertures (15) or slits (5) in one (or two) of their electrodes, usually by resonant excitation, and the ions leaving the trap can be measured as a mass spectrum at an ion detector. Scan speeds of 30,000 atomic mass units per second and even more can be achieved, in mass ranges up to 3,000 atomic mass units, with mass resolutions better than a quarter atomic mass unit.
Depending on the time needed to fill the ion trap with ions and on the width of the mass scan, four to eight mass spectra can be acquired per second when no further ion manipulations are required, which is favorable for any combination of the ion trap mass spectrometer with separation processes like gas or liquid chromatography (GC or LC). The spectrum acquisition works successfully when the trap is not overloaded with ions. Favorable numbers of ions amount to 1,000 to 10,000 ions; the space charge of larger amounts of ions destroys a high-quality ejection process, strongly diminishing the mass resolution. If much less ions are loaded, the quality of the spectrum suffers from a low signal-to-noise ratio. To keep the acquisition rate for mass spectra as high as possible, any further processes of ion manipulation like isolation or fragmentation should be designed to be as short as possible.
Within this document, the terms “mass”, “heavy ions”, “high mass”, “light ions”, or “low mass” always refer to charge-related masses m/z, m being the mass, and z being the number of unbalanced elementary charges of the ion. Number z has the physical dimension of a pure number; therefore m/z has the physical dimension of a mass.
Analytical ions of interest (the “desired ions”), as generated in usual types of ion sources, are sometimes present only in low concentrations in complex mixtures of ions (see, for instance, the schematic presentation in FIG. 4). If the desired ions are present only in amounts of 0.1 percent, the ion trap has to be overloaded with a million ions in order to keep, after successful isolation, a thousand desired ions in the trap. To keep 10,000 ions, and to care for some losses during isolation, even more than ten million ions have to be filled into the ion trap prior to isolation. 107 ions are about the maximum number of ions which can be filled into an ion trap against the effect of space charge.
Ions with charge-related masses m/z below a so-called cut-off mass (m/z)cut-off cannot be stored at all in RF ion traps; these ions are already removed during the filling process. The cut-off mass (m/z)cut-off is directly proportional to the RF voltage. As is well-known by specialists in the field, light ions above the cut-off mass gather in the center, and heavier ions surround the center in layers like onion shells.
In heavily overloaded RF ion traps (105 to 107 ions), resonant excitation no longer works correctly because space charge couples the movement of ions inside the trap. A strong excitation has to be applied to eliminate ions and energy from excited ions dissipates immediately to ions not directly excited and the desired ions are usually removed together with undesired ions.
But even in RF ion traps which are not heavily overloaded (104 to 105 ions), resonant excitation does not always successfully remove ions. Particularly extremely heavy ions (high m/z) are hard to excite sufficiently for removal because their low oscillation frequency in the pseudopotential well requires a high excitation voltage and a long excitation time, and the slow oscillations of the heavy ions with their high collision cross sections are continuously damped in the damping gas inside the ion trap. These heavy ions often remain within the ion trap and disturb the following processes, i.e., the reactions of the desired ions and the analysis of the reaction products.
Ions can also be isolated by application of superimposed quadrupolar RF and quadrupolar DC fields, similar to the superposition of RF and DC voltages in quadrupole mass filters. But here the process of isolation is rather slow because the ions in the exact center of the trap do not see any fields; these ions can only be eliminated after they have drifted, by incidental thermal movements, to sufficiently wide locations outside the center. In addition, the electronics needed for this method are rather complex and expensive. Consequently, applications of this method are not known.
The use of sharp DC voltage pulses at single endcap electrodes of three-dimensional ion traps has become known for purposes of ion activation and fragmentation (S. A. Lammert and R. G. Cooks: “Pulsed Axial Activation in the Ion Trap: a New Method for Performing Tandem Mass Spectroscopy (MS/MS)”, Rapid Comm. Mass Spectrom., Vol. 6, 528-530 (1992)). The short pulses of typically two microsecond length consist of a superimposed mixture of frequencies, and these frequencies can excite ions to oscillations and even fragment ions by subsequent collisions with damping gas.
DC voltages at endcaps can also be used for other purposes as disclosed in B. M. Prentice et al., 58th ASMS Conference 2010, Salt Lake City: “DC Potentials Applied to Endcap Electrodes of 3-D Ion Traps for Increased Ion Injection Efficiency and Manipulation of Ion/Ion Reactions”. In this presentation, the use and effect of DC voltages on endcap electrodes has been investigated. This work states that there exist “Sporadic reports of dipolar DC in ion trap literature, but little systematic work has been reported in the open literature”. Among other applications, single electrode DC voltages were used by the authors to help isolation by resonant ejection. It was found, that the peak-to-peak voltages needed for resonant ejection could be lowered by about 30 percent by simultaneous application of DC voltages, thereby reducing “off-resonance heating” of the ions. In this context off-resonance heating means an undesired excitation of the desired ions.